Molecules and mechanisms
of epigenetics
Basis of epigenetics
Adult stem cells know their fate!
For example: myoblasts can form muscle cells only.
Hematopoetic cells only become blood cells.
.....but all those cells have identical genome sequences!
Modern definition of epigenetics is as follows: it is nonsequence dependent inheritance and chromatine changes.
How can just paternal or maternal traits be expressed in
offspring? This is called genetic imprinting.
How can females express only one X chromosome per cell?
We observe some changes in gene expression that are
heritable!
Inactive X has unacetylated histone H4
Epigenetics is based on
four different mechanisms
(so far…..)
1. DNA Methylation
2. Chromatin remodelling
3. Histone modification
4. RNA interference/interactions
Two faces of chromatin control
DNA from zygote to adult – methylation state
Chromatin restricts accessibility of the genome
Horn and Peterson, Science, 2002
Euchromatin
Transcriptionally active, less compacted
Heterochromatin
Less transcriptionally active, very compacted
a) constitutive heterochromatin
centromeres, telomeres
b) facultative heterochromatin
rDNA, transposons, inactive X chromosome
Condensed chromatin state depends on
cytosine methylation
Daug Brutlag, 2011
Two most obvious states of chromatin
Importance of CpG Sequences in CpG
Islands Near Promoters
Architecture of Epigenome
DNA is compacted through interactions
with proteins
DNA and chromatine proteins is a template
for epigenetic phenomena
Numerous post-translational histone
modifications
Histone acetylation
Acetylation of the lysine residues at the N terminus of histons removes positive charges,
thereby reducing the affinity between histones and DNA. This makes RNA polymerase and
transcription factors easier to access the promoter region. Therefore, in most cases,
histone acetylation enhances transcription while histone deacetylation represses
transcription.
Histone acetylation is catalyzed by histone acetyltransferases (HATs) and histone
deacetylation is catalyzed by histone deacetylases (denoted by HDs or HDACs). Several
different forms of HATs and HDs have been identified. Among them, CBP/p300 is probably
the most important, since it can interact with numerous transcription regulators.
Importance of acetylation at the histon level
Acetylation of histones serves as epigenetic marker within chromatin. Several reports have
shown that one modification has the tendency to influence whether another modification will
take place.
Modifications of histones can not only cause secondary structural changes at their specific
points, but can cause many structural changes in distant locations which inevitably affects
function.
As the chromosome is replicated, the modifications that exist on the parental chromosomes
are handed down to daughter chromosomes. The modifications, as part of their function, can
recruit enzymes for their particular function and can contribute to the continuation of
modifications and their effects after replication has taken place.
It has been shown that, even past one replication, expression of genes may still be affected
many cell generations later.
Histone Methylation
Unlike acetylation, histone methylation does not alter the charge of the modified
residues and it is therefore less likely to directly alter nucleosomal interactions
required for chromatin folding. This probably explains why histone methylation can
either repress or activate transcription depending on location.
Arginine methylation of histone H3 and H4 promotes transcriptional activation,
whereas lysine methylation of histone H3 and H4 is implicated in both transcriptional
activation and repression, depending on the methylation site. In addition, lysine
residues can be methylated in the form of mono-, di-, or tri-methylation, providing
further functional diversity to each site of lysine methylation. For example, trimethylation on K4 of Histone H3 (H3K4me3) is generally associated with
transcriptional activation, whereas tri-methylation on K9 and K27 of histone H3
(H3K9me3 & H3K27me3) are generally associated with transcriptional repression.
For many years, histone methylation was thought to be irreversible as it is a stable
mark propagated through multiple cell divisions. However, it was recently shown that,
similarly to histone acetylation, methylation is an actively regulated and reversible
process.
Histone code hypothesis
The Histone code hypothesis suggests the idea that patterns of post-translational
modifications on histones, collectively, can direct specific cellular functions.
Chemical modifications of histone proteins often occur on particular amino acids. This specific
addition of single or multiple modifications on histone cores can be interpreted by
transcription factors and complexes which leads to functional implications. This process is
facilitated by enzymes such as HATs and HDACs that add or remove modifications on histones,
and transcription factors that process and "read" the modification codes. The outcome can be
activation of transcription or repression of a gene. For example, the combination of
acetylation and phosphorylation have synergistic effects on the chromosomes overall
structural condensation level and, hence, induces transcription activation of immediate early
gene.
Experiments investigating acetylation patterns of H4 histones suggested that these
modification patterns are collectively maintained in mitosis and meiosis in order to modify
long-term gene expression. The acetylation pattern is regulated by HAT and HADC enzymes
and, in turn, sets the local chromatin structure. In this way, acetylation patterns are
transmitted and interconnected with protein binding ability and functions in subsequent cell
generation.